RnoINT0118343 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140971821-140972391:+
Coord C1 exon
chr7:140971821-140971929
Coord A exon
chr7:140971930-140972240
Coord C2 exon
chr7:140972241-140972391
Length
311 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATG
5' ss Score
8.99
3' ss Seq
TTAATCCCGTGTCTTTTCAGGAA
3' ss Score
11.83
Exon sequences
Seq C1 exon
GCGGGCAGAACAGACTTTTGGGGACCTGGAGGTCTGGGCTGTGGTCCCTGAGAGGGATAGAAAAGAAGTTTATGATGATGTCCTCTTCTTCCTGGCCAAGAAGGAGAAG
Seq A exon
GTAATGGACAATCACTGGCTGGATTTTCCCGCCCTCAATTTCTTGTAGACCTGGCTACTCATTTCTCTACTCAGTGTCCCTTCTCTTGAATGGGAAGCTGGTGTGGAACTTTTTCCTTCCCCACTTCCGCACTGGGCCAATAACCCTGGGTGGAGGGGGGGGCAAGGAGGACACTGGTCTGTGACTTGGAATTCCTCTTCTTCCTGGAACACAGAAGTCTTGAATGTTGTTTCCTAAGGTCTTCTAGCTGCCTCCTTTCCCCAGTTCCTCCTTTGCCAGCCCTGCCTCACTTTAATCCCGTGTCTTTTCAG
Seq C2 exon
GAACAAGCCAAGCAGCTCCGGCGTCGAAACATCCAAGCCCTGAAGAGCATCCTGGATGGGATGAGTAGTGTCAACTTCCAAACCACATGGTCCCAGGCCCAGCAGTACCTCATGGATAACCCCAGCTTTGCTCAGGACCAGCAGCTGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0394210=DTW=PD(4.2=13.5)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGCAGAACAGACTTTTGGG
R:
AGCTGCTGGTCCTGAGCAAAG
Band lengths:
254-565
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]